Biology subjects

Kooyers, N. J.

Publications and source records attributed to Kooyers, N. J..

11 recordsLinked to original sources

bioRxiv2026

Harnessing historical collections to reconstruct the invasion history of Microstegium vimineum (Poaceae)

The evolutionary processes underlying successful invasions are often difficult to disentangle. Historical collections provide a temporal perspective, offering great potential to reconstruct invasion histories and identify the processes driving invasions. Japanese stiltgrass (Microstegium vimineum) is an invasive C4 grass introduced to eastern North America over a century ago and now established in 31 USA states. To reconstruct its invasion history, we leveraged low-coverage whole-genome sequencing of 142 herbarium and 330 contemporary samples spanning the temporal and spatial extent of the North American invasion and the native range in Asia. We identified three independent introductions in the USA: an awnless form in the South and two independent introductions of awned forms in the North, with limited admixture among introductions across space and time. In both regions, we observed high genetic diversity in the earliest available collections despite demographic bottlenecks and identified several putative selective sweeps in or near flowering-time genes, suggesting rapid evolution in the introduced range. Our analyses support separate invasions in the USA, likely facilitated by standing genetic variation and selection, but provide little support for admixture playing a major role. Our study highlights the power of historical collections to uncover the processes and mechanisms underlying successful biological invasions.

evolutionary biology↗

bioRxiv2026

Regional gene-environment association models improve insights into agents and targets of selection by climate in Mimulus guttatus

Genotype-environment association (GEA) approaches identify genetic variants that likely contribute to adaptation along environmental gradients. These associations can inform predictive models of maladaptation risk and evolutionary rescue in future climates. However, because population structure and climate parameters often co-vary, tradeoffs arise between accounting for population structure to reduce false positive associations and removing true positives. Here, we examine whether conducting GEA analyses at multiple spatial scales provides more informative associations by mitigating confounds between population structure and environment, and we evaluate what factors influence how congruent GEA results are across regions. We performed GEA analyses for climate parameters on genome resequencing data obtained for 110 annual populations of the common monkeyflower, Mimulus guttatus. We find that more genetic variation was specifically attributable to environmental variation in regional GEA models compared to a full-range model, and that agents of selection differ considerably in importance among regions and range-wide. Few genetic targets of selection shared across regions were detected, yet all regions possess ample standing genetic variation for most environment-associated variants, suggesting that regional differences in climate breadth may be a primary cause of this incongruence. In combination with a genome-wide association study for several climate-associated phenotypes, we also find that regulators of flowering repressors in the FLC/MAF gene family often harbor adaptive variation in this species. Together, our results suggest that GEA analyses of widespread species considerably benefit from examining both range-wide and regional trends to more fully capture and understand the agents and targets of climate adaptation.

evolutionary biology↗

bioRxiv2026

Herbarium genomics reveal signatures of colonization history, lineage turnover, and adaptation during invasion

O_LIA key challenge in invasion biology is dissecting the roles of colonization history, admixture, and selection on invasion success. However, it is often difficult to determine the sources and locations of introduction events as well as the timing and magnitude of gene flow and selection using genomics datasets from contemporary samples. C_LIO_LIWe disentangle the evolutionary processes acting during the North American invasion of Trifolium repens (white clover) using low-coverage whole genome sequencing from 513 herbarium specimens originally collected between 1838-2018. C_LIO_LIIntroduction history paralleled European colonization patterns. The earliest collected samples had predominantly Belgian and British ancestry, with increasing French and Spanish contributions over time in the Mid-Atlantic and South. Genomic diversity increased significantly through time likely driven by admixture between independently introduced lineages. In lowest latitude regions, there is a strong shift in dominant ancestry with limited admixture (i.e., lineage turnover). Putatively adaptive loci exhibited protracted shifts in allele frequency during the invasion, consistent with contemporary clines. C_LIO_LIOur study demonstrates the power of herbarium genomics to provide spatiotemporal insight into recent evolutionary history. We find a complex invasion history that includes multiple introductions, lineage turnover, and admixture that increased genetic diversity and likely facilitated adaptation in this now cosmopolitan plant. C_LI

plant biology↗

bioRxiv2025

Rapid adaptation follows experimental assisted gene flow in subset of annual monkeyflower populations

Assisted gene flow, the human-facilitated movement of species within its range, has the potential to increase genetic diversity and facilitate adaptation for climate-threatened populations. However, concerns regarding outbreeding depression and gene swamping have limited the application of assisted gene flow, and experimental tests have been largely confined to simulations and laboratories. We conducted a landscape-scale manipulation, planting seeds and seedlings from historically hotter and drier source populations into climate-threatened populations of the common yellow monkeyflower (Mimulus guttatus) and tracked change in genomes, phenotypes, and fitness. Within three generations, source alleles introgressed into half of the target populations. Assisted gene flow increased fitness in one experimental block of populations and slightly decreased fitness in a second block. Fitness increases were associated with flowering earlier and producing fewer trichomes. Greater fitness changes occurred in populations where seeds rather than seedlings were introduced. Both the amount of introgression and fitness changes were heterogeneous between years, suggesting that temporal fluctuations in climate likely impact initial introgression and success of assisted gene flow. Initial introgression from source populations was low across the genome, limiting concerns of gene swamping. Our results are generally consistent with theoretical models, and provide cautious optimism for an often-maligned conservation strategy.

evolutionary biology↗

bioRxiv2025

A field experiment assessing the roles of drought, herbivory, and local climate on cyanogenesis cline formation and local adaptation in Trifolium repens

Projecting how a population will adapt to environmental changes requires a mechanistic understanding of the specific biotic and abiotic factors that impose selection on that population. In white clover (Trifolium repens), clines in an antiherbivore defense mechanism, hydrogen cyanide (HCN), form via variation in selection imposed by the environment. However, the specific environmental factors that select for or against chemical defense phenotypes in white clover remain unresolved. We performed a field experiment in high and low latitude study sites, with a factorial manipulation of precipitation and herbivory at each site. These factors are hypothesized to be important in driving HCN cline formation, so we investigated their effects on fitness of a white clover F3 recombinant population, segregating for the alleles underlying the HCN chemical defense phenotype. Surprisingly, we found precipitation and herbivory either did not drive differential selection on HCN or its metabolic components, or did not impose selection in a manner consistent with the maintenance of observed HCN clines. Instead, we find that the production only one of the metabolic components of HCN, cyanogenic glycosides, resulted in a fitness advantage, even when lacking the ability to produce HCN. This was most prominent at the northern study site, which is again contrary to expectations. These results suggest additional physiological roles that cyanogenic glycosides may play in adaptation and the evolutionary ecology of white clover. This study highlights the importance of experimental manipulations of environmental factors to understand how selection acts on genes underlying important phenotypic traits, often in unexpected ways.

evolutionary biology↗

bioRxiv2024

Adaptation to climate in the native and introduced ranges of a cosmopolitan plant

Climate change and the global spread of non-native species are two of the most significant threats to biodiversity and ecosystem function. Both these phenomena subject populations to novel conditions, either in space (species introductions) or in time (climate change), yet the role of adaptation in how populations respond to these rapid environmental shifts is poorly understood. We conducted a large-scale trans-continental common garden experiment using white clover (Trifolium repens, Fabaceae) to test whether adaptive evolution to spatiotemporal variation in climate could contribute to the ecological success of one of the most widespread plant species in the world. Individuals from 96 populations of Trifolium repens (white clover) from both its native (Europe) and introduced (North America) ranges were planted into four experimental common gardens located in northern (Uppsala, Sweden) and southern (Montpellier, France) Europe, and northern (Mississauga, Canada) and southern (Lafayette, USA) North America. We recorded plant sexual and clonal fitness in each common garden and assessed whether the strength of local adaptation differed between the native and introduced ranges and whether populations are rapidly adapting to climate change. Results show that local adaptation was only evident when populations were transplanted into common gardens located in the same range (native or introduced) from which they originated and was driven by stronger selection (due to climatic factors rather than herbivory) at lower latitudes in both ranges. Our results indicate rapid local adaptation across a large latitudinal gradient in introduced T. repens populations, along with an associated adaptation cost when transplanted back into the native range. We also find evidence of an adaptation lag in the northern common garden in the introduced range, with plants from historically warmer climates exhibiting the greatest fitness. These findings support two major conclusions: 1) white clover can rapidly adapt to spatial variation in climate in its introduced range as well as the native range, and 2) despite rapid adaptation to novel environments, introduced white clover populations are not keeping pace with rapid climate change. Overall, our results provide insight into the role of adaptation in facilitating the ecological success of non-native species in a rapidly changing world. Open Research StatementData are provided for peer review. All data involved in this study is available on the GitHub page for LJA (https://github.com/ljalbano/transcontinental_common_garden).

evolutionary biology↗

bioRxiv2024

Evolution of drought resistance strategies following the introduction of white clover (Trifolium repens L.)

Background and AimsSuccess during colonization likely depends on growing quickly and tolerating novel and stressful environmental conditions. However, rapid growth, stress avoidance, and stress tolerance are generally considered divergent physiological strategies. MethodsWe evaluate how white clover (Trifolium repens) has evolved to a divergent water regime following introduction to North America. We conduct RNAseq within a dry-down experiment utilizing accessions from low and high latitude populations from native and introduced ranges, and assess variation in dehydration avoidance (avoidance of wilting) and dehydration tolerance (ability to survive wilting). Key ResultsIntroduced populations are better at avoiding dehydration, but poorer at tolerating dehydration than native populations. There is a strong negative correlation between avoidance and tolerance traits and expression of most drought-associated genes exhibits similar tradeoffs. Candidate genes with expression strongly associated with dehydration avoidance are linked to stress signaling, closing stomata and producing osmoprotectants. However, genes with expression linked to dehydration tolerance are associated with avoiding excessive ROS production and toxic bioproducts of stress responses. Several candidate genes show differential expression patterns between native and introduced ranges, and could underlie differences in drought resistance syndromes between ranges. ConclusionsThese results suggest there has been strong selection following introduction for dehydration avoidance at the cost of surviving dehydration.

evolutionary biology↗

bioRxiv2023

Does urbanization lead to parallel demographic shifts across the world in a cosmopolitan plant?

Urbanization is occurring globally, leading to dramatic environmental changes that are altering the ecology and evolution of species. In particular, the expansion of human infrastructure and the loss and fragmentation of natural habitats in cities is predicted to increase genetic drift and reduce gene flow by reducing the size and connectivity of populations. Alternatively, the "urban facilitation model" suggests that some species will have greater gene flow into and within cities leading to higher diversity and lower differentiation in urban populations. These alternative hypotheses have not been contrasted across multiple cities. Here, we used the genomic data from the Global Urban Evolution project (GLUE), to study the effects of urbanization on non-adaptive evolutionary processes of white clover (Trifolium repens) at a global scale. We found that white clover populations presented high genetic diversity and no evidence of a reduction in Ne linked to urbanization. On the contrary, we found that urban populations were less likely to experience a recent decrease in effective population size than rural ones. In addition, we found little genetic structure among populations both globally and between urban and rural populations, which showed extensive gene flow between habitats. Interestingly, white clover displayed overall higher gene flow within urban areas than within rural habitats. Our study provides one of the largest comprehensive tests of demographic effects of urbanization and our results contrast the common perception that heavily altered and fragmented urban environments will reduce the effective population size and genetic diversity of populations and contribute to their isolation.

evolutionary biology↗

bioRxiv2023

Haplotype-resolved, chromosome-level assembly of white clover (Trifolium repens L., Fabaceae)

BackgroundWhite clover (Trifolium repens L.; Fabaceae) is an important forage and cover crop in agricultural pastures around the world, and is increasingly used in evolutionary ecology and genetics to understand the genetic basis of adaptation. Historically, improvements in white clover breeding practices and assessments of genetic variation in nature have been hampered by a lack of high-quality genomic resources for this species, owing in part to its high heterozygosity and allotetraploid hybrid origin. FindingsHere, we use PacBio HiFi and chromosome conformation capture (Omni-C) technologies to generate a chromosome-level, haplotype-resolved genome assembly for white clover totaling 998 Mbp (scaffold N50 = 59.3 Mbp) and 1 Gbp (scaffold N50 = 58.6 Mbp) for haplotypes 1 and 2, respectively, with each haplotype arranged into 16 chromosomes (8 per subgenome). We additionally provide a functionally annotated haploid mapping assembly (968 Mbp, scaffold N50 = 59.9 Mbp), which drastically improves on the existing reference assembly in both contiguity and assembly accuracy. We annotated 78,174 protein-coding genes, resulting in protein BUSCO completeness scores of 99.6% and 99.3% against the embryophyta_odb10 and fabales_odb10 lineage datasets, respectively. ConclusionsWe provide two white clover genome assemblies as part of this project: (1) a haplotype-resolved, chromosome-level assembly, and (2) a functionally annotated haploid mapping assembly. These assemblies place white clover among the best sequenced legumes to date, and one of the best assemblies for a plant of recent polyploid origins. This work promises to facilitate ongoing and future work in agricultural and evolutionary genetics in this agronomically and ecologically important species.

genomics↗

bioRxiv2023

Demographic consequences of an extreme heatwave are mitigated by spatial heterogeneity in an annual monkeyflower

Heatwaves are becoming more frequent and intense with climate change, but the demographic and evolutionary consequences of heatwaves are rarely investigated in herbaceous plant species. We examine the consequences of a short but extreme heatwave in Oregon populations of the common yellow monkeyflower (Mimulus guttatus) by leveraging a common garden experiment planted with range-wide populations and observational studies of eleven local populations. In the common garden, 89% of seedlings died during the heatwave including >96% of seedlings from geographically-local populations. Some populations from hotter and drier environments had higher fitness, however others from comparable environments performed poorly. Observational studies of local natural populations drastically differed in the consequences of the heatwave - one population was completely extirpated and nearly half had a >50% decrease in fitness. However, a few populations had greater fitness during the heatwave year. Differences in mortality corresponded to the impact of the heatwave on soil moisture - retention of soil moisture throughout the heatwave led to greater survivorship. Our results suggest that not all populations experience the same intensity or degree of mortality during extreme events and such heterogeneity could be important for genetic rescue or to facilitate the distribution of adaptive variants throughout the region.

ecology↗

bioRxiv2021

Human urine alters methicillin-resistant Staphylococcus aureus virulence and transcriptome

Gram-positive methicillin-resistant Staphylococcus aureus (MRSA) is an emerging cause of hospital-associated urinary tract infections, especially in catheterized individuals. Despite being rare, MRSA-UTI are prone to potentially life-threatening exacerbations such as bacteremia that can be refractory to routine antibiotic therapy. Hence, MRSA-UTI is an important of research topic. To delineate molecular mechanisms governing MRSA urinary pathogenesis, we exposed three S. aureus strains, of which two were MRSA, to human urine and analyzed virulence characteristics and gene expression. We also analyzed MRSA-1369 transcriptome following cultivation in human urine for 2h. Our results reveal that human urine induces global changes in MRSA transcriptome, marked by changes in genes encoding proteins involved in metabolic pathways, virulence, and transcriptional regulators. In addition, in vitro assays also showed that human urine alters, in a strain-specific manner, adherence to human bladder epithelial cells and fibronectin, hemolysis of sheep RBCs, and surface hydrophobicity. In summary, our results provide first important insights into how the urine may specifically alter MRSA physiology in turn facilitating MRSA survival in the nutrient-limiting and hostile urinary microenvironment. ImportanceMethicillin-resistant Staphylococcus aureus (MRSA) is an uncommon cause of urinary tract infections (UTI) in the general population. However, it is important to understand MRSA pathophysiology in the urinary tract because isolation of MRSA in urine samples is often secondary to potentially life-threatening MRSA bacteremia. In this report, we describe that cultivation in human urine alters MRSA global gene expression and virulence. We hypothesize that these alterations may aid MRSA adapt to the nutrient-limiting, immunologically hostile conditions within the urinary tract.

microbiology↗